There was just a weird curve where you play for quite a few hours and it remains quite easy, and then you realise it's just a really really really long game and you're entering the more difficult mid/late-game stage. I think it was Ch3 when that happened for me. Definitely got ass kicked a fair few times.
I remember the same when I did my first violent case, and instead of having everyone just be jolly, I lost most of my squad within the first few rounds. Irene can run around solo most of the time when built properly, but sometime during Chapter 3 enemies start being strong enough to just club her to death in a single round, and even her second life won't save her anymore. I remember having to finish most of that first challenging violent case with a fucking Shield NPC and Anne. After that mission I decided that having her heal is just a waste when she can nuke entire screens worth of enemies every other round instead and also burn vigor, which is really damn useful and something not a whole lot of characters can do. I think the difficulty increase is simply due to player expectation not being that the "tutorial" phase of the game lasts 10-15hours, or that the game is as long as it is to finish. I would even argue that it is one of the weaker points of the game, as the game itself doesn't start picking up the pace and difficulty until you get your 5th member, which takes quite a lot of time. I know that I got a bit impatient with being teased a bunch of different named characters and then having to play with the same pre-generated NPCs for ~10hours or so. But once you get past that point and start running most missions with just your squad and a handful of expendables, boy does it get amazing.